The polymerase chain reaction (PCR) is based on repeated cycles of denaturation of double stranded DNA, followed by oligonucleotide primer annealing to the DNA template, and primer extension by a DNA polymerase (e.g., see Mullis et al U.S. Pat. Nos. 4,683,195, 4,683,202 and 4,800,159). The oligonucleotide primers used in PCR are designed to anneal to opposite strands of the DNA, and are positioned so that the DNA polymerase-catalysed extension product of one primer can serve as a template strand for the other primer. The PCR amplification process results in the exponential increase of discrete DNA the length of which is defined by the 5′ ends of the oligonucleotide primers. Specificity in standard PCR, amplification of DNA is principally determined by the sequence of the primers in combination with the temperature at which the annealing step is conducted. For closely related sequences, additional approaches have been incorporated to provide selective amplification. PCR performed with standard primers cannot distinguish one sequence from a closely related sequence if the primers used can bind to both sequences to generate an extension substrate. U.S. Pat. No. 7,618,773 and Rand et al., Nucl. Acids Res. 33:e127 (2005) describe a “headloop” suppression PCR method taught to suppress amplification of non-amplification target variants by extension of a 3′ stem-loop to form a hairpin structure that can no longer provide a template for further amplification.